BMRB Entry 5691

Click here to enlarge.

PDB ID: 1ny4
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS, SPARTA
BMRB Entry DOI: doi:10.13018/BMR5691
MolProbity Validation Chart

NMR-STAR file interactive viewer.
NMR-STAR v3 text file.
XML gzip file.
RDF gzip file.
All files associated with the entry

Nicholas Rego and David Koes
3Dmol.js: molecular visualization with WebGL
Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

Select model:

I am color blind

Download raw data. Direct link to this display. Help

Title:

Solution Structure of the 30S ribosomal protein S28E from Pyrococcus horikoshii. Northeast Structural Genomics Consortium target JR19

Deposition date:

2003-02-12

Original release date:

2003-02-25

Authors:

Aramini, James; Cort, John; Huang, Y.; Xiao, Rong; Acton, Thomas; Ho, Chi; Shih, Liang-yu; Kennedy, Micheal; Montelione, Gaetano

Citation:

Citation: Aramini, James; Huang, Y.; Cort, John; Goldsmith-Fischman, S.; Xiao, Rong; Shih, Liang-yu; Ho, Chi; Liu, J.; Rost, B.; Honig, B.; Kennedy, M.; Acton, Thomas; Montelione, Gaetano. "Solution NMR structure of the 30S ribosomal protein S28E from Pyrococcus horikoshii. " Protein Sci. 12, 2823-2830 (2003).
PubMed: 14627742

Assembly members:

Assembly members:
RS28_PYRHO, polymer, 82 residues, 9365 Da.

Natural source:

Natural source: Common Name: P. horikoshii Taxonomy ID: 53953 Superkingdom: Archaea Kingdom: not available Genus/species: Pyrococcus horikoshii

Experimental source:

Experimental source: Production method: recombinant technology Host organism: Esherichia coli Vector: pET21

Entity Sequences (FASTA):

Entity Sequences (FASTA):
RS28_PYRHO: MAEDEGYPAEVIEIIGRTGT TGDVTQVKVRILEGRDKGRV IRRNVRGPVRVGDILILRET EREAREIKSRRAAALEHHHH HH

Data sets:

assigned_chemical_shifts
- JR19_set_1
coupling_constants
- JR19_JNH_1

Data type	Count
1H chemical shifts	543
13C chemical shifts	333
15N chemical shifts	76
coupling constants	45

Time Domain Data

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
Hide all

Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	RS28_PYRHO, JR19	1

Entities:

Entity 1, RS28_PYRHO, JR19 82 residues - 9365 Da.

1

MET

ALA

GLU

ASP

GLU

GLY

TYR

PRO

ALA

GLU

2

VAL

ILE

GLU

ILE

GLY

ARG

THR

GLY

THR

3

THR

GLY

ASP

VAL

THR

GLN

VAL

LYS

VAL

ARG

4

ILE

LEU

GLU

GLY

ARG

ASP

LYS

GLY

ARG

VAL

5

ILE

ARG

ASN

VAL

ARG

GLY

PRO

VAL

ARG

6

VAL

GLY

ASP

ILE

LEU

ILE

LEU

ARG

GLU

THR

7

GLU

ARG

GLU

ALA

ARG

GLU

ILE

LYS

SER

ARG

8

ARG

ALA

LEU

GLU

HIS

9

HIS

Samples:

sample_1: RS28_PYRHO, [U-100% 13C; U-100% 15N], 1.0 mM; MES 20 mM; NaCl 100 mM; CaCl2 5 mM; DTT 10 mM; NaN3 0.02%; D2O 5%

sample_2: RS28_PYRHO, [U-100% 13C; U-100% 15N], 1.0 mM; MES 20 mM; NaCl 100 mM; CaCl2 5 mM; DTT 10 mM; NaN3 0.02%; D2O 100%

sample_3: RS28_PYRHO, [U-5% 13C; U-100% 15N], 1.0 mM; MES 20 mM; NaCl 100 mM; CaCl2 5 mM; DTT 10 mM; NaN3 0.02%; D2O 5%

sample_conditions_1: pH: 6.5; temperature: 293 K

Experiments:

Name	Sample	Sample state	Sample conditions
1H,15N-HSQC (regular)	not available	not available	sample_conditions_1
1H,15N-HSQC (NH2 only)	not available	not available	sample_conditions_1
1H,15N-HSQC (full SW)	not available	not available	sample_conditions_1
1H,13C-HSQC (aliph)	not available	not available	sample_conditions_1
1H,13C-HSQC (arom)	not available	not available	sample_conditions_1
3D 1H-15N NOESY	not available	not available	sample_conditions_1
3D 1H-13C NOESY (aliph)	not available	not available	sample_conditions_1
3D 1H-13C NOESY (arom)	not available	not available	sample_conditions_1
4D 13C NOESY	not available	not available	sample_conditions_1
HNCO	not available	not available	sample_conditions_1
CBCA(CO)NH	not available	not available	sample_conditions_1
HNCACB	not available	not available	sample_conditions_1
CBCACO(CA)HA	not available	not available	sample_conditions_1
HA(CA)NH	not available	not available	sample_conditions_1
HA(CACO)NH	not available	not available	sample_conditions_1
(H)CC(CO)NH TOCSY	not available	not available	sample_conditions_1
H(CCCO)NH TOCSY	not available	not available	sample_conditions_1
HcCH COSY	not available	not available	sample_conditions_1
HcCH TOCSY	not available	not available	sample_conditions_1
HNHA	not available	not available	sample_conditions_1
1H,13C-HSQC (high res)	not available	not available	sample_conditions_1
H/D exchange (6 min)	not available	not available	sample_conditions_1
H/D exchange (60 min)	not available	not available	sample_conditions_1
H/D exchange (8 hrs)	not available	not available	sample_conditions_1

Software:

VNMR v6.1B - spectrometer, acquisition

NMRPipe v2.1 - data processing

Sparky v3.106 - peak picking

AUTOASSIGN v1.9 - automated assignment of backbone 1H, 13C, 15N chemical shifts

AUTOSTRUCTURE v1.1.2 - automated NOESY assignment, structure determination

HYPER v3.2 - data analysis

TALOS v2.1 - data analysis

DYANA v1.5 - structure refinement

PDBStat v3.27 - structure analysis

NMR spectrometers:

Varian INOVA 800 MHz
Varian INOVA 750 MHz
Varian UNITY 600 MHz
Varian INOVA 600 MHz
Varian INOVA 500 MHz

SWISS-PROT	P61030 Q8U159 P61029
REF	NP_579097 NP_126358 NP_143359
EMBL	CAB49589
GenBank	AAL81492
PDB	1NY4
DBJ	BAA30603